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Kennedy Airport is finally doing something about overcrowding – it’s booting the more than 100 feral cats cluttering its runways.

Despite protests from animal activists, the Port Authority has begun a kitty crackdown – targeting first a group living near a parking lot for Delta Airline’s cargo facility.

Smaller round-ups have been going on since the summer, when the agency, with the help of federal wildlife officials, began trapping colonies of cats elsewhere on the grounds.

Many are descendants of pets that escaped their cages after arriving at the airport. Others were abandoned by owners.

For decades, they have made the overgrown fields, parking lots, hangars and depots their home. Workers and animal activists estimate there are six feral-cat “colonies” spread throughout JFK’s 5,000 acres.

They rely on the kindness of cat-loving airport workers, who leave a canned food around the grounds.

“Some of the guys call them and pet them,” said Narine Sriprasad, a shuttle-bus driver who says about 20 cats live under a depot’s engine room. “They are not scared. They’re friendly.”

The PA says getting rid of the cats will make it safer for passengers and air crews.

“This is ultimately a safety issue and an unsafe condition being created,” said PA spokesman Pasquale DiFulco, noting that food left for the cats can attract birds, which fly into jet engines.

“Birds and aeronautical areas do not mix,” he said.

“We are not going to jeopardize the safety of more than 46 million air passengers who use JFK Airport.”

But cat lovers are howling, since the felines will be turned over to Animal Care and Control and most euthanized.

Her group met with PA officials and the airport’s wildlife biologist and volunteered to trap, neuter and vaccinate the cats free of charge. Some cats would be put up for adoption and others returned to the airport. But the offer was turned down.

The airport was very tolerant of the cats until recently, said a worker who helped get 58 in one colony neutered during the last few years. “Then we were told we are not allowed to feed them,” he said.